Jefferson and Madison led a revolutionary fight for complete separation of church and state. Their reasons probed the basic relation between religion and democracy

In his own terms, Jefferson claimed to be a Christian —but he assuredly was not one according to Dr. Abercrombic’s standards, or for that matter according to the doctrine of any organized Christian church, unless it was the fledgling Unitarian. He rejected, he wrote, “the immaculate conception of Jesus, his deification, the creation of the world by him, his miraculous powers, his resurrection and visible ascension, his corporeal presence in the Eucharist, the Trinity, original sin, atonement, regeneration, election, orders of Hierarchy, etc.” He thought of Christ as a great reformer, author of “a system of the most sublime morality which has ever fallen from the lips of man”—but human rather than divine. To be a Christian, for Jefferson, was simply to follow the system of ethics taught by Christ, uncontaminatecl by what he considered the additions, adulterations, and distortions of those who came after. And Jefferson thought he had an easy touchstone for distinguishing Jesus’ original teachings from the dross. All that was needed was the “free exercise of reason”: with that, the genuine precepts of the Master would never be found to disagree.

To orthodox clergymen and theologians this was heresy; it was, many of them angrily charged, a mere disguise for atheism. As a prominent political figure, Jefferson often suffered from his refusal to accept traditional Christianity, even though he tried to keep his religious views largely to himself. His skepticism toward anything alleged to be supernatural was misunderstood, and his high regard for Christian ethics was usually ignored. Shocking stories circulated long before he became a presidential candidate, and their currency grew with his fame. John Trumbull, the great painter of the Revolution, told one about a dinner party at Jefferson’s home in 1793, when the future President sat “smiling and nodding approbation” while Congressman William Giles of Virginia—a fellow skeptic—”proceeded so far … as to ridicule the character, conduct and doctrines of the divine founder of our religion.” This was unquestionably an exaggeration, but it suggests Jefferson’s reputation at the time. When he was presidential runner-up in 1796, a minister in Connecticut took note of the event in a prayer before his congregation: “O Lord! wilt Thou bestow upon the Vice President a double portion of Thy grace, for Thou knowest he needs it.” In the campaign of 1800 Jefferson’s “infidelity” was an easy target for Federalist orators and pamphleteers.

Yet there is little doubt that Jefferson held a profound belief in a Supreme Being. In a fashion typical of eighteenth-century intellectuals, he held it not on implicit faith, but as a reasoned conclusion based on evidence and deduction. “I hold (without appeal to revelation),” he once wrote to John Adams, “that when we take a view of the universe, in its parts, general or particular, it is impossible for the human mind not to perceive and feel a conviction of design, consummate skill, and indefinite power in every atom of its composition.” Newton and his contemporaries in the seventeenth century had magnificently demonstrated that man lived in a universe of precise mathematical law and order; it seemed scientifically evident to most thinkers in the following era that such a cosmic design could come only from the hand of a divine Creator.

It was a long way from the theology of traditional Christianity, this idea of an invisible but demonstrable God whose existence was proved only by His handiwork; for “He” was now a nearly impersonal power, responsible for the origin and laws of the universe, but not interfering in its operation once the myriad wheels of the great machine had been set in motion. This was “Nature’s God,” as Jefferson phrased it in the Declaration of Independence; and to him and many others the religion appropriate to Nature’s God must be natural, not supernatural, in its foundations. Deism, or “natural religion,” expressed their theological creed, not a Christianity based on revelation, mystery, and miracle.

Some men—notably a prominent group in France including Diderot, d’Alembert, Condorcet, and the Baron d’Holbach—went further, postulating an automatic universe, operating by inexorable natural laws, but utterly devoid of God or God’s purpose. Jefferson was inclined to resist this surge toward atheism, yet it is only justice to the true character of his mind to emphasize that his attitude was far from fanatical. He was never an absolutist, even on the question of God’s existence. His creed of intellectual freedom was much too firm for that, and at worst he saw no alarming threat in atheism. Before he went to France to be United States minister from 1784 to 1789, he had already considered the effects of full disbelief. “It does me no injury for my neighbor to say there are twenty Gods, or no God,” he observed in his Notes on Virginia (1782). “It neither picks my pocket nor breaks my leg.” And writing to his young nephew, Peter Carr, from Paris in 1787, he urged him to make reason his guide: "… call to her tribunal every fact, every opinion. Question with boldness even the existence of a God; because, if there be one, he must more approve of the homage of reason, than that of blindfolded fear.”